chr3-150324831-G-A

Variant names:

• chr3-150324831-G-A
• rs4301033
• ENST00000692847.3:n.76+6116C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000692847.3(LINC01214):​n.76+6116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,172 control chromosomes in the GnomAD database, including 1,239 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1239 hom., cov: 32)
• Consequence: LINC01214 ENST00000692847.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.54
• Publications: 16 publications found

Genes affected

LINC01214 (HGNC:49650): (long intergenic non-protein coding RNA 1214)

ENSG00000297695 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986141	XR_001740958.1	n.1981+16432G>A		intron_variant	Intron 1 of 2
LOC107986141	XR_007096127.1	n.1981+16432G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01214	ENST00000692847.3	n.76+6116C>T		intron_variant	Intron 1 of 1
LINC01214	ENST00000716186.1	n.41+6116C>T		intron_variant	Intron 1 of 3
LINC01214	ENST00000716187.1	n.623+16275C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17233 AN: 152054 Hom.: 1237 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0556

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.113 AC: 17255 AN: 152172 Hom.: 1239 Cov.: 32 AF XY: 0.110 AC XY: 8190 AN XY: 74404

African (AFR) AF: 0.194 AC: 8054 AN: 41494

American (AMR) AF: 0.0787 AC: 1204 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0552 AC: 266 AN: 4816

European-Finnish (FIN) AF: 0.0672 AC: 712 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0915 AC: 6224 AN: 68004

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.0983 Hom.: 3436

Bravo AF: 0.120

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		3.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4301033; hg19: chr3-150042618;